# Fluidigm Singular Analysis Toolset

## Documentation for package ‘fluidigmSC’ version 3.6.2

- DESCRIPTION file.

## Help Pages

A B C D E F G H I M P R S T U V W

## -- A --

addOutlierFromFile | Remove a Set of Samples to the Outlier List
addOutlierFromList | Remove a Set of Samples to the Outlier List
addOutlierFromName | Remove a Sample to the Outlier List
analyzeGeneDetection | Gene Detection Per Sample
ANOVA | Analysis of Variance
applyHC | Hierarchical Clustering Analysis
applyPCA | Apply a PCA Model to New Expression Data
autoAnalysis | Analyze Expression Data to Obtain Differentially Expressed Genes

## -- B --

boxPlotByGenes | Box Plot by Genes
boxPlotBySamples | Box Plot by Samples

## -- C --

clearExcludedExpDataColumnNames | Clear Excluded Column Names for Reading Tab Delimited Linear Exp Data Files
clearExcludedExpDataRowNames | Clear Excluded Row Names for Reading Tab Delimited Linear Exp Data Files
clearGeneGroupColorAndSymbols | Clear the Customized Sample Group Color and Symbol Settings
clearSampleGroupColorAndSymbols | Clear the Customized Sample Group Color and Symbol Settings
clusterPCAScore | Cluster PCA Score
clustertSNE | Cluster tSNE Result
createGeneListFromGeneNames | Gene List from Gene Names

## -- D --

display3DPCAScore | 3D PCA Score Plot
displayANOVAPValues | Display ANOVA P-Values
displayCorrGenes | Display gene expression profile of co-expressed genes of selected
displayHC | Display Hierarchical Clustering
displayPCAGeneScores | Display PCA Gene Scores
displayPCALoading | PCA Loading Plot
displayPCAScore | PCA Score Plot
displayPCAScree | PCA Scree Plot
displaytSNE | tSNE Plot

## -- E --

excludeExpDataColumnByName | Excluded Column Names for Reading Tab Delimited Linear Exp Data Files
excludeExpDataRowByName | Excluded Row Names for Reading Tab Delimited Linear Exp Data Files
exportHCHeatmap | Export Hierarchical Clustering Analysis Heatmap

## -- F --

findCorrGenesFromFile | Find Co-Expressed Genes
findCorrGenesFromList | Find Co-Expressed Genes
findCorrGenesFromName | Find Co-Expressed Genes
firstRun | Install Dependent Packages
fluidigmSC | Fluidigm Singular Analysis Toolset v3.6.2
foldChangeAnalysis | Fold Change Analysis Between Two Sample Groups

## -- G --

getGeneClusterByThreshold | Obtain Gene Cluster by Threshold
getSampleClusterByThreshold | Obtain Sample Cluster by Threshold
getTopANOVAGenes | Get Top ANOVA Genes
getTopPCAGenes | Get Top Ranked PCA Genes

## -- H --

HC | Hierarchical Clustering Analysis

## -- I --

identifyGeneClusters | Identify Gene Clusters
identifyOutliers | Identify Outliers
identifySampleClusters | Identify Sample Clusters

## -- M --

mergeExpData | Merge EXP Objects
mergeGeneList | Merge Gene Lists
mergeSampleList | Merge Sample Lists
mergeVariantList | Merge Variant Lists

## -- P --

pairwiseANOVASummary | ANOVA Analysis Summary
pairwiseScatterPlotBetweenSampleGroups | Correlation Scatter Plot of Sample Groups
PCA | Principal Component Analysis

## -- R --

readCtExp | Read Ct Expression Data
readData | Read Data
readExpObject | Read EXP Object Files
readLinearExp | Read Linear Expression Data
readVCF | Read VCF Data
readVCObject | Read VC Object Files
removeGene | Remove a Gene
removeGeneGroup | Remove a Group of Genes
removeGenesByCtExp | Remove Genes with Low Expression
removeGenesByLinearExp | Remove Genes with Low Expression
removeSample | Remove a Sample
removeSampleGroup | Remove a Group of Samples
resetGeneList | Reset Gene List
resetHCMarginFactor | Reset HC Display Margin
resetSampleList | Reset Sample List
restoreAllOutlier | Restore Outliers
restoreOutlierFromList | Restore Outliers from an Outlier List
restoreOutlierFromName | Restore an Outlier
retainGeneGroup | Retain a Group of Genes
retainSampleGroup | Retain a Group of Samples

## -- S --

saveData | Save Data
scExpFunctions | Quick Help for Singular Expression Analysis Functions
scFunctions | Quick Help for Singular R Functions
scVarFunctions | Quick Help for Singular Variant Analysis Functions
scVariables | Quick Help for Current Variables used in data analysis by Singular package
setGeneGroupColorAndSymbols | Customize Gene Group Color and Symbol Settings
setHCMarginFactor | Set HC Display Margin
setSampleGroupColorAndSymbols | Customize Sample Group Color and Symbol Settings
summaryExp | Summarize an Expression Object

## -- T --

tSNE | T-Distributed Stochastic Neighbor Embedding

## -- U --

updateGeneListFromFile | Update Gene List
updateGeneListFromList | Update Gene List
updateLod | Recalculates the Log2 Expression (Log2EX) with a new LoD.
updateSampleListFromFile | Update Sample List
updateSampleListFromList | Update Sample List
updateSampleListFromName | Update Sample List

## -- V --

vcAddOutlierFromFile | Remove a Set of Samples to the Outlier List
vcAddOutlierFromList | Remove a Set of Samples to the Outlier List
vcAddOutlierFromName | Remove a Sample to the Outlier List
vcAutoAnalysis | Analyze Variant Data via GUI to Obtain Variants of Interest
vcClearSampleGroupColorAndSymbols | Clear the Customized Sample Group Color and Symbol Settings
vcClearVariantGroupColorAndSymbols | Clear the Customized Variant Group Color and Symbol Settings
vcDisplayFisherTestResults | Display Manhattan plot for Fisher test result of variant calls
vcDisplayHC | Display Hierarchical Clustering of Variant Data
vcEvalSampleGroupVariants | Evaluate Variant-Calling Performance for Sample Groups
vcEvalSampleVariants | Evaluate Variant-Calling Performance for Individual Samples
vcExportHCHeatmap | Export Heatmap of Hierarchical Clustering Analysis
vcGetCommonVariantListWithCallFromSampleGroup | Get Common Variant List with Calls from a Sample Group
vcGetFailVariantsFromVariantCall | Get Failed Variants From Variant Call
vcGetFilterVariantListByVariantQuality | Get High-Quality Variant List
vcGetPassVariantsFromVariantCall | Get Passed Variants From Variant Call
vcGetSignificantVariants | Get Significant Variant List in Case-Control Study
vcGetVariantListBySampleGroupAlleleFrequency | Get Variant List with Common GT in a Sample Group
vcGetVariantListWithCallFromSample | Get Variant List with Calls from a Sample
vcHC | Hierarchical Clustering Analysis for Variant Data
vcIdentifySampleClusters | Identify Sample Clusters
vcIdentifySigVariants | Identify Mutations or Variants at Single-Cell Resolution
vcIdentifyVariantClusters | Identify Variant Clusters
vcMergeVCObj | Merge VC Objects
vcPerformFisherTest | Perform Fisher EXACT Test for VC data
vcRemoveLowQualitySamples | Remove Low-Quality Samples from Sample List of VC
vcRemoveSampleGroup | Remove a Group of Samples
vcRemoveSamples | Remove a Sample
vcRemoveVariant | Remove a Variant
vcRemoveVariantGroup | Remove a Variant Group
vcResetSampleList | Reset Sample List
vcResetVariantList | Reset Variant List
vcRestoreAllOutlier | Restore All Outliers
vcRestoreOutlierFromList | Restore Outliers from an Outlier List
vcRestoreOutlierFromName | Restore an Outlier in VC Object
vcRetainSampleGroup | Retain a Group of Samples
vcRetainVariantGroup | Retain a Group of Variants
vcSetSampleGroupColorAndSymbols | Customize Sample Group Color and Symbol Settings
vcSetVariantGroupColorAndSymbols | Customize Variant Group Color and Symbol Settings
vcUpdateSampleListFromFile | Update Sample List
vcUpdateSampleListFromList | Update Sample List
vcUpdateSampleListFromName | Update Sample List From Sample Name
vcUpdateVariantListByVariantQuality | Update VC Object According to its Variant Quality
vcUpdateVariantListFromFile | Update Variant List
vcUpdateVariantListFromList | Update Variant List
vcUpdateVariantListFromVariantAnnotation | Update Variant List from VCF Variant Annotations
vcUpdateVariantQuality | Determine Quality of Variant Calls in Samples
violinPlotByGenes | Violin Plot by Genes
violinPlotBySamples | Violin Plot by Samples

## -- W --

writeVCF | Save Variant Data as VCF File